Protein evidence

The protein evidence shows a chromosome-centric summary of the evidence for protein existence for all predicted human protein-coding genes. Three sources for evidence have been used, Protein existence (PE) data from UniProt and neXtProt, and transcriptomics and proteomics data from HPA. Read more about the assessment and scoring of evidence in the Evidence details section below. Click on a chromosome bar and the evidence summary for each gene along the chromosome will be displayed.

Chromosome summary

Evidence summary

HPA evidence

UniProt evidence

NeXtProt evidence

Chromosome	Genes with protein evidence
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Chromosome	Genes with antibody-based evidence
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Chromosome	Genes with UniProt-based evidence
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Chromosome	Genes with neXtProt-based evidence
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All chromosomes

Evidence details

Protein evidence is calculated for each gene based on three different sources: UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence); and a Human Protein Atlas antibody- or RNA based score (HPA evidence). In addition, for each gene, a protein evidence summary score is based on the maximum level of evidence in all three independent evidence scores (Evidence summary).

All scores are classified into the following categories:

Evidence at protein level
Evidence at transcript level
No evidence
Not available

UniProt evidence is based on UniProt protein existence data, which uses five types of evidence for the existence of a protein. All genes in the classes "Experimental evidence at protein level" or "Experimental evidence at transcript level" are classified into the first two evidence categories, whereas genes from the "Inferred from homology", "Predicted", or "Uncertain" classes are classified as "No evidence". Genes where the gene identifier could not be mapped to UniProt from Ensembl version 109 are classified as "Not available".

neXtProt evidence is based on neXtProt protein existence data, which uses five types of evidence for the existence of a protein. All genes in the classes "Experimental evidence at protein level" or "Experimental evidence at transcript level" are classified into the first two evidence categories, whereas genes from the "Inferred from homology", "Predicted", or "Uncertain" classes are classified as "No evidence". Genes where the gene identifier could not be mapped to neXtProt from Ensembl version 109 are classified as "Not available".

The HPA evidence is calculated based on the manual curation of Western blot, tissue profiling and subcellular location as well as transcript profiling. All genes with Data reliability "Supported" in one or both of the two methods immunohistochemistry and immunofluorescence, or standard validation "Supported" for the Western blot application (assays using over-expression lysates not included) are classified as "Evidence at protein level". For the remaining genes, all genes detected at nTPM > 1 in at least one of the HPA consensus, brain or immune cell sets used in the RNA-seq analysis based on HPA and GTEx are classified as "Evidence at transcript level". The remaining genes are classified as "No evidence".